Biomolecules & Bioethics Reviewer (Walpole)

Biomolecules General Biology 1 | STEM 12-Walpole Polymerization Polymer Large macromolecules, long chain-like molecules, of Carbohydrates, Proteins and Nucleic Acids are Polymers Is a long molecule consisting of many similar/identical building block...

Biomolecules General Biology 1 | STEM 12-Walpole Polymerization Polymer Large macromolecules, long chain-like molecules, of Carbohydrates, Proteins and Nucleic Acids are Polymers Is a long molecule consisting of many similar/identical building blocks linked by covalent bonds, like the cars of a train Each class of is made up of different types of monomers but all the chemical mechanisms involved in creating/breaking them down are through enzymes (macromolecules that speed up/facilitate chemical reactions) Monomer They are the repeating units/building blocks of all polymers and are smaller molecules that also have their own functions Bonds (Covalent) Two types of chemical bonds: Ionic & Covalent bonds Ionic bonds entails the donation or transfer of electrons from one atom to another; between a metal & non-metal Covalent bonds, the type primarily used in biomolecules, involves the sharing of the same electrons between atoms; between non metals Carbon Atom Atomic number of 6 (6 protons and 6 electrons in a neutral state) 4 valence electrons Can form four covalent bonds Fundamental component of all organic molecules, including carbohydrates, lipids, proteins, and nucleic acids; has the ability to form long chains and complex branched structures that lead to a vast diversity of organic compounds. Readily forms compounds with hydrogen, oxygen, nitrogen, and halogens, and has the ability to form stable and varied covalent bonds that makes carbon compounds crucial for life. Carbon Ring Structure where carbon atoms are connected in a closed loop, forming the backbone of many organic and biomolecules. These rings can be: ○ Aliphatic: single bonds like cyclohexane, or ○ Aromatic: alternating double bonds, like benzene. Common Ring Structure: 6 carbons in a ring Vary in size, from small, strained rings (e.g., cyclopropane) to large, flexible macrocycles, and may include other elements Appears in carbohydrates, nucleic acids, and steroids STEM 12-Walpole, General Biology Academics Committee | Page 1 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Vitamins B and C Both B Vitamins and Vitamin C are water-soluble vitamins meaning they are absorbed in the body’s tissues and not stored, unlike their lipid counterparts. Organic compounds vital for growth and nutrition in small amounts; cannot be produced in the body. B Vitamins: ○ B Vitamins are not one kind of vitamin but a vast array of different enzymes that aid in maintaining proper bodily functions. This includes metabolism, healthy skin cells, creation of new blood cells, transporting energy, and keeping brain function in check. Vitamin C: ○ Vitamin C plays a vital role in keeping the body healthy and functioning, as it is the main nutrient the body consumes in creating new tissue to replace old or damaged tissue in the form of collagen, this includes blood vessels, muscle, and cartilage. Minerals They are inorganic micronutrients classified further into two groups Marcominerals, and Microminerals. Macrominerals are minerals that need to be consumed in amounts greater than 100mg per day: Calcium, Phosphorus, Magnesium, Sodium, Potassium, Chloride, and Sulfur Microminerals can be consumed in amounts less than 100mg per day: Iron, Zinc, Copper, Selenium, Iodine, Chromium, and Molybdenum They aid in regulating bodily functions and growth such as being the building blocks of bone, regulating water balance, aiding in metabolism, and influencing nerve and muscle function. ADEK These are lipid/fat-soluble vitamins and are absorbed and stored in the body as they dissolve in organic solvents such as lipids and are transported as such (as fat). STEM 12-Walpole, General Biology Academics Committee | Page 2 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Vitamin A, plays a key role in the maintenance of both eyesight and the immune system, while also aiding in the reproductive system and overall growth and development. Vitamin D, this vitamin helps regulate calcium and phosphorus and is a key component in maintaining the body’s bone and muscle structure and function. Vitamin E, this vitamin has antioxidant properties and is very important for vision, reproduction, blood, brain, and skin. Vitamin K, aids in blood clotting which hastes the speed of the recovery of injuries, and strengthens bones, and cognitive functions. Acids & Bases Act as catalysts to speed up polymerization reactions and the pH of a reaction can influence the solubility, stability and reactivity of monomers Acids have a pH level of below 7, while bases have a pH higher than 7, a pH 7 substance is considered neutral Acids produce hydrogen ions (donating), while Bases absorb hydrogen ions (accepting) When dissolved in water, acids will give off hydrogen ions, while bases will give off hydroxyl ions Dehydration The reaction from two monomers connecting with each other or with a polymer is a condensation reaction, where two molecules covalently bond with the loss of a molecule If the molecule lost is a water molecule, then it is a dehydration reaction Each reactant contributes part of the water molecule released (ex. One provides a Hydroxyl group of OH and the other provides H) & this is repeated as monomers are added to the chain Hydrolysis The process of monomers breaking down polymers is called Hydrolysis, and is the reverse of dehydration synthesis The bond is broken as a water molecule is added, with each monomer connecting to either the H or Hydroxyl Group STEM 12-Walpole, General Biology Academics Committee | Page 3 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Organic Molecule Are molecules that contain carbon-hydrogen and/or carbon bonds in which carbon is covalently commonly bonded with hydrogen, oxygen & nitrogen. Inorganic Molecule Do not contain carbon-hydrogen bonds (with some exceptions like carbonates, cyanides, and oxides of carbon). Compound examples: salts, metals, acids, bases, and simple molecules like water and carbon dioxide. Typically simpler in structure and are not limited to the diverse bonding patterns seen in organic chemistry Carbohydrates Carbohydrates Serve as fuel and building material Include sugars and polymers of sugars Consist of carbon, hydrogen, and oxygen, often in the proportion 1:2:1 Sugars (Simple Carbohydrates) a. Monosaccharide Usually contain five or six carbon atoms Glucose (C6H12O6): most abundant monosaccharide Major fuel for cellular work and their exoskeletons serve as raw material for the synthesis of other types of molecules such as amino and fatty acids Monosaccharides come in either a ring form or a linear form Depending on the amount of carbon atoms, can be classified into triose, pentose, hexose STEM 12-Walpole, General Biology Academics Committee | Page 4 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Linear form Structure (D-Glucose, R-Glucose) Ring form Structure (ribose, glucose, fructose): a1. Ribose Pentose Component of nucleotides; backbone of RNA (ribonucleic acid) Also present in ATP (adenosine triphosphate), the primary energy carrier in cells Not commonly found in the diet as free sugar; synthesized in the body via the pentose phosphate pathway Involved in nucleic acid and energy metabolism rather than as a direct energy source like glucose Used in RNA; in DNA, the sugar component is deoxyribose, which differs by one lacking oxygen a2. Glucose Hexose Primary energy source for cells; directly used in glycolysis Found in fruits, vegetables, and as a component of starch Highly soluble in water and can be readily utilized for energy STEM 12-Walpole, General Biology Academics Committee | Page 5 of 29  Biomolecules General Biology 1 | STEM 12-Walpole a3. Fructose Hexose Used by the body for energy; is metabolized primarily in the liver. It can be converted into glucose or stored as fat. Found in fruits, honey, and high-fructose corn syrup. a4. Galactose Hexose Converted to glucose in the liver Found in dairy products as part of lactose. a5. Triose Contains three carbon atoms Examples: Glyceraldehyde and Ketotriose dihydroxyacetone. a6. Pentose Contains five carbon atoms involved in the structure of nucleic acids (RNA and DNA) and energy metabolism (pentose phosphate pathway) Examples: Ribose, Arabinose, Lyxose, and Xylose. a7. Hexose Contains six carbon atoms Examples: Dextrose, Galactose, Mannose, Fructose, Glucose b. Disaccharide Two monosaccharides joined by dehydration synthesis (covalent bond) b1. Sucrose Glucose + Fructose Made up of both Glucose & Fructose, this disaccharide is usually found in common table sugar. Is found in the natural world through fruits, vegetables and nuts. STEM 12-Walpole, General Biology Academics Committee | Page 6 of 29  Biomolecules General Biology 1 | STEM 12-Walpole b2. Maltose Glucose + Glucose Also known as ‘malt sugar’ and is usually found and used in molasses and fermentation. b3. Lactose Glucose + Galactose More commonly known as ‘milk sugar’ and is found in dairy products. Complex Carbohydrates a. Polysaccharides (“many sugars”) Carbohydrates composed of hundreds to thousands of sugar units for each molecule Polysaccharides are further grouped into storage and structural : i. Storage polysaccharides are used to store energy ii. Structural polysaccharides form the structural framework of the cell a1. Starch A common method of storing glucose in plants such as potatoes, corn, peas and lentils a2. Glycogen Stored form of energy and glucose in animals STEM 12-Walpole, General Biology Academics Committee | Page 7 of 29  Biomolecules General Biology 1 | STEM 12-Walpole a3. Amylopectin Non-Crystallizable form of starch Quick energy storage for plants Highly branched structure; more rapid access to glucose units a4. Amylose Crystallizable form of starch Straight chain of glucose molecules that is an energy storage molecule in plants, but less readily mobilized than Amylopectin No branching a5. Cellulose An important structure made up of polysaccharides used in maintaining the structure of a plants’ cell wall and helps in the facilitation of cell division STEM 12-Walpole, General Biology Academics Committee | Page 8 of 29  Biomolecules General Biology 1 | STEM 12-Walpole a6. Chitin Structural support in the exoskeletons of arthropods (like insects and crustaceans) and in fungal cell walls Tough and flexible; not digestible by humans but can be broken down by certain organisms. b. Oligosaccharides Carbohydrates contain 2 or more (2-10) monosaccharides, which can be any sugar monomer. These are absorbed in the small intestine as its individual components through hydrolysis Glycosidic Bond These are covalent bonds of a ring-shaped/ring-form sugar/carbohydrates to other molecules (condensation reaction) Carbonyl Chemical Formula of C=O (Carbon atom double bonded with an Oxygen atom) Primary members are called aldehydes, ketones, and carboxylic acids. Lipids Lipids Lipids are biomolecules are that insoluble in water but soluble in organic solvents like hexane or chloroform; they are all united by their hydrophobic quality Lipids primarily store and transfer energy in the body, absorb ADEK, and make hormones Typically consist of hydrocarbon regions with relatively non-polar C–H bonds STEM 12-Walpole, General Biology Academics Committee | Page 9 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Glycerol An alcohol with a chemical formula of C₃H₈O₃ with each of its 3 carbons bonded with a hydroxyl group Fatty Acid Carboxylic acids with long aliphatic (organic open chain structure) chains/skeletons made of hydrocarbons (usually 16-18 carbons in length) Fatty acids produced naturally have even carbon atoms and are usually unbranched The carbon at the end of the group is attached to a carboxyl group (double bond to one oxygen, single bonded with one oxygen and hydrogen) Saturated Fatty Acid These are fatty acids that lack a Carbon double bond (C=C) in their aliphatic chain, and so as many hydrogen atoms as possible are bonded to the carbon skeleton (hence saturated with hydrogen) ○ Stearic acid: 18 carbon atoms long STEM 12-Walpole, General Biology Academics Committee | Page 10 of 29  Biomolecules General Biology 1 | STEM 12-Walpole ○ Palmitic acid: 16 carbon atoms long ○ Myristic acid: 14 carbon atoms long ○ Lauric acid: 12 carbon atoms long ○ Capric acid: 10 carbon atoms long ○ Caprylic acid: 8 carbon atoms long ○ Caproic acid: 6 carbon atoms long Can increase the presence of Low-Density Lipoproteins (LDL) from the loss/combination of or into one fatty acid making it a phospholipid; sticks to arteries causing heart disease Unsaturated Fatty Acid These are fatty acids that have at least one Carbon double bond (C=C) in their aliphatic chain Each double bond may be cis (hydrogen around the double bond is on same plane) or trans configuration (hydrogen around the double bond is not on same plane) Types of Unsaturated fats: Monounsaturated and Polyunsaturated Since kinks prevent a close linking of each carbon atom and make them liquid at room temp Fat Consists of two main components: a glycerol backbone and 3 fatty acid tails Aids in insulation, energy storing, and padding in an organism Formed when a glycerol molecule creates an ester linkage with a fatty acid, a dehydration reaction occurs where the fats separate from water via a release of hydrogen molecules to form water (also the reason why fats separate from oil) STEM 12-Walpole, General Biology Academics Committee | Page 11 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Triglyceride (Fat & Oil) General Structure Trans fats have hydrogens on opposite sides of a kink; come from turning a liquid unsaturated fat to solid and is very unhealthy Cis fats have hydrogens on the same side of a kink Oil Made of hydrocarbons It is any nonpolar chemical substance that is is hydrophobic and lipophilic Same chemical structure as fats, just liquid at room temperature Fat vs Oil If there are more saturated fatty acids: FAT STEM 12-Walpole, General Biology Academics Committee | Page 12 of 29  Biomolecules General Biology 1 | STEM 12-Walpole If there are more unsaturated fatty acids: OIL Triglyceride Other name for fat Function as the main form of lipid and energy storage in the human body They come from unused calories and provide energy for the body when needed Nonpolar lipid Phospholipid Polar lipid A glycerol backbone, 2 fatty acids only instead of 3 in fats, and 1 phosphate group that is connected to an alcohol (e.g. choline) Functions as a barrier/protection for the cell against environmental insults and enables multiple cellular processes Phospholipid Chemical & General Structure Phosphate group A phosphorus atom covalently bonded to four oxygen atoms (one of the bonds is double bonds); highly reactive and negatively charged ○ Energy storage and transfer; ATP (adenosine triphosphate); breaking the phosphate bond releases energy for cellular functions. ○ Addition of phosphate groups to proteins (phosphorylation) regulates protein activity; cell signaling and metabolism. ○ Phospholipids; phosphate group forms the hydrophilic head of the phospholipid. Choline STEM 12-Walpole, General Biology Academics Committee | Page 13 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Stabilizes the phospholipid as its positive charge reacts with the negatively-charged phosphate group Maintains healthy cell function in the nervous system and the liver Water-soluble compound (often grouped with B-vitamins) A source of methyl groups needed for many steps in metabolism Two major phospholipids vital for cell membranes and are contained in phospholipid heads with a phosphate group where it is hydrophilic Ethyl chain to a nitrogen atom with a positive charge Eggs, meat and poultry, fish, legumes, broccoli Steroids Made of carbon rings and plays an essential role in aiding in physiological function; one carbon skeleton attached to 4 rings Examples: Sex Hormones, Bile Acid, Cholesterol Steroid Structure (Cholesterol as Example) with 4 carbon rings and a side chain Cholesterol is synthesized in the liver a key part of animal cell membranes, helping regulate their fluidity STEM 12-Walpole, General Biology Academics Committee | Page 14 of 29  Biomolecules General Biology 1 | STEM 12-Walpole an unhealthy diet can easily contribute to high cholesterol levels, increasing the risk of cardiovascular disease; saturated fats stimulate the liver to produce more cholesterol in animals Stabilizes membrane protein Phospholipid Bilayer This is the layer that separates the cell from its environment and controls what enters and exits the cell via Bilayer since it is made up of 2 sets of opposite-facing lipid molecules (see image below) Hydrophilic Heads It is connected to the glycerol component and is hydrophilic meaning it attracts water/polar molecules and allows proteins and other biomolecules to transfer in and out the cell These are on the exterior/surface protecting the hydrophobic tails Hydrophobic Tails These are nonpolar and are in the interior of the cell and are made of the hydrophobic fatty acids The hydrophobic and packed nature of the tails creates a barrier that prevents the diffusion of large or charged molecules such as water from passing into the cell Phospholipid Bilayer and Phospholipid Kink or Kink-turn; a point in the helix where there is a sharp change in the direction of the helix axis Double bonds in liquid unsaturated fats create kinks that prevent the fat molecules from packing tightly Helps phospholipids stay fluid and allows transport between the membrane by wiggling/moving cx Differentiates between Saturated and Unsaturated fats. STEM 12-Walpole, General Biology Academics Committee | Page 15 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Ester Bond Covalent bond between an alcohol group (–OH) in Glycerol and a carboxylic acid group (–COOH) in Fatty Acids. During bond formation a water molecule (H₂O) is released. The process of creating an ester is called esterification. Found in lipids, where fatty acids are linked to glycerol by ester bonds; also important in synthetic materials, like polyester. Ester Bond between Glycerol and Fatty Acids Proteins Proteins (Proper) From the Greek ‘proteios’ meaning ‘first’ or ‘primary’ and accounts for 50% of the dry mass of all cells STEM 12-Walpole, General Biology Academics Committee | Page 16 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Involved in speeding up chemical reactions, defense, storage, transport, cellular communication or structural support Enzymes, a type of protein, act as catalysts that speed up chemical reactions Made of amino acids (monomers) where the bond between amino acids is called a peptide bond A polymer of amino acids is called a polypeptide, and proteins are biomolecules made up of one or more polypeptides Carboxyl Group (--COOH) Acts as an acid (can donate H+) because the covalent bond between oxygen and hydrogen is so polar One of 7 key functional groups, carbon atom double bonded to oxygen and single bonded with a hydroxyl group Compound Names: Carboxylic acid and organic acid Amino Group (--NH2) Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms) One of 7 key functional groups, nitrogen single bond with two hydrogen groups Compound Name: Amine Central Carbon Each biomolecule contains an asymmetric Central Carbon atom, also known as the α-carbon, to where an amino group & carboxyl group attach to The remaining two bonds are typically with hydrogen and another R chain group to form an amino acid STEM 12-Walpole, General Biology Academics Committee | Page 17 of 29  Biomolecules General Biology 1 | STEM 12-Walpole R group Attaches to the α-carbon alongside the amino and carboxyl group to form an amino acid Also known as the side chain, varies with each amino acid and can range from a single hydrogen atom to a complex carbon skeleton The properties of each side chain determine the unique characteristics of its respective amino acid 20 R-groups Peptide Bond The covalent bond between different amino acids, forms a dipeptide (di meaning two) Occurs during a condensation reaction where the amino group of one amino acid reacts with the carboxyl group of another The resulting reaction releases H2O and results in the formation of a peptide bond (-CO-NH-) Peptide Bond (Dehydration Process) Peptide STEM 12-Walpole, General Biology Academics Committee | Page 18 of 29  Biomolecules General Biology 1 | STEM 12-Walpole A short chain of amino acids, typically between 2 - 50 Polypeptide (Amino Acid Polymers) A much longer chain of amino acids, typically more than 50 Can represent a part of or the entirety of a protein, where the carboxyl group (C-Terminus) of one amino acid (N-Terminus) is adjacent to the amino group of another Can fold into a functional shape, and can fold into higher-order structures (primary, secondary, tertiary, quaternary) Enzymes Specialized macromolecules, typically proteins (but NOT always) that speed up chemical reactions Lower the energy requirement for reactions Possesses an active site for the Lock-and-Key Model Substrate A specialized molecule that binds to an enzyme at a specific region: the active site Enzyme-Substrate Complex formed after an enzyme and substrate binds and is crucial for the catalytic process Lock-and-Key Model A model that displays enzyme action and how an enzyme bonds with and fits into a specifically-shaped substrate at their active site Once the substrate and active site bond, the reaction is carried out by the enzyme and products are released Substrate is the Key that is shaped perfectly to fit into the Enzyme or Lock, where each substrate fits just one enzyme perfectly Primary Structure STEM 12-Walpole, General Biology Academics Committee | Page 19 of 29  Biomolecules General Biology 1 | STEM 12-Walpole A linear chain/sequence of amino acids linked together to form a polypeptide chain The order of the amino acids determines the shape & function of the protein. The primary backbone of a protein Secondary Structure Arises from interactions of hydrogen bonds between amino acids Can form sheets and helices: a. Alpha Helix - a helical, coiled structure, hydrogen bonding at every fourth amino acid b. Beta Sheets - the hydrogen bonds result in an almost linear sheet Tertiary Structure Arises from hydrophobic interactions of some amino acids Hydrophobic R-groups of amino acids are located or nested in the middle of the polypeptide Starting from here, the protein is now functional and shows the overall shape of a polypeptide Quaternary Structure Arises from interaction between multiple polypeptide chains of a protein Different polypeptide chains interacting with each other (it is not necessary that all participating polypeptide chains have tertiary structure, some can be secondary) Shows the overall structure of a protein STEM 12-Walpole, General Biology Academics Committee | Page 20 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Nucleic acids Nucleic Acids (proper) Macromolecules that exist as polymers known as polynucleotides Polynucleotides are made up of monomers known as nucleotides which each contain 1 pentose sugar, 1 nitrogenous base & 1-3 phosphate groups A portion of a nucleotide with no phosphate group is a nucleoside Phosphate group A phosphorus atom is covalently bonded to four oxygen atoms (one of the bonds is double bonds, all other oxygen atoms must have a negative charge if not bonded with another); highly reactive and negatively charged ○ Link nucleotides together in nucleic acids (DNA and RNA); genetic material. Pentose sugar 5 carbon sugar Deoxyribose for DNA, C5H10O4 Ribose for RNA ○ The difference between the sugars is the presence of the hydroxyl group on the second carbon of the ribose and hydrogen on the second carbon of the deoxyribose (so deoxyribose is "missing" an -OH group). ○ C5H10O5 Nitrogenous base A molecule that contains nitrogen and has the properties of a base (accepts hydrogen ions) There are two types of Nitrogenous bases, pyrimidine bases (one ring) and purine bases (two rings). The pyrimidine bases are cytosine (both), thymine (DNA only) and uracil (RNA only). ○ Pyrimidine A single-ring structure or six-membered ring of carbon & nitrogen atoms composed of four carbon atoms and two nitrogen atoms. STEM 12-Walpole, General Biology Academics Committee | Page 21 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Cytosine (C), Thymine (T), Uracil (U) ○ Purine Two-carbon nitrogen rings (six membered with a five membered ring) composed of five carbon atoms and four nitrogen atoms Adenine (A) and Guanine (G) Hydrogen bond Each DNA molecule consists of two nucleotide chains wrapped around each other in a double helix and held together by hydrogen bonds. This hydrogen bonding involves only the nitrogenous bases. A dipole-dipole attraction between molecules, or an attraction between two atoms that already participate in other chemical bonds. An attraction between a hydrogen atom covalently bonded with very electronegative atoms like N, O, Cl and F Phosphodiester bond Covalent bond of a phosphate of one nucleotide and the hydroxyl (OH) group attached to the 3′ carbon of the sugar in an adjacent nucleotide Forms the sugar-phosphate backbone of DNA Location of the Phosphodiester bond Deoxyribose A pentose sugar for DNA Has one less oxygen atom than ribose on the second carbon ring and at the 2’ carbon position hence deoxy- Rotates to the right Formula: C₅H₁₀O₄ More stable Phosphate group attaches to 5’ carbon position, Nitrogenous base attaches to 1’ carbon position STEM 12-Walpole, General Biology Academics Committee | Page 22 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Ribose A pentose sugar for RNA Has one more oxygen atom than deoxyribose on the second carbon ring and at the 2’ carbon position (hydroxyl group: -OH which makes it more reactive/less stable) Formula: C₅H₁₀O₅ Phosphate group attaches to 5’ carbon position, Nitrogenous base attaches to 1’ carbon position Deoxyribonucleic acid DNA proper; consists of a sugar phosphate backbone and its base pairs Contains all the genetic information of an organism inherited from its parents & gives the codes that program all of a cell’s activities, as well as instructions to replicate it and the organism. Ribonucleic acid RNA proper; consists of a single strand of sugar phosphate and its single nucleobases Through DNA, RNA is synthesized and used in protein synthesis STEM 12-Walpole, General Biology Academics Committee | Page 23 of 29  Biomolecules General Biology 1 | STEM 12-Walpole mRNA Messenger RNA; they carry the coding sequences for protein synthesis or transcripts transcribed from DNA tRNA Transfer RNA; they carry amino acids to the ribosomes rRNA Ribosomal RNA; they make up the structure of ribosomes Base pair Pairs of bases that attach themselves to each other in a DNA strand via hydrogen bonding along a sugar-phosphate backbone and where only certain bases can attach to each other Adenine In ATP (Adenosine triphosphate) with a ribose and three phosphate groups Composed of a 5-sided and 6-sided ring as a Purine Binds to Thymine in DNA, Uracil in RNA with TWO HYDROGEN BONDS Thymine In TTP (Thymidine triphosphate) with deoxyribose and three phosphate groups Pyrimidine and consists only of a 6-sided ring Does NOT exist in RNA Guanine In GTP (Guanosine triphosphate) with a ribose and three phosphate groups Composed of a 5-sided and 6-sided ring as a Purine Binds to Cytosine with THREE HYDROGEN BONDS STEM 12-Walpole, General Biology Academics Committee | Page 24 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Cytosine In CTP (Cytidine triphosphate) with deoxyribose and three phosphate groups Pyrimidine and consists only of a 6-sided ring Nitrogenous Base Pairings: Grooves Runs continuously along the entire length of the DNA molecule Arises from the antiparallel arrangement of the two backbone strands ○ MINOR GROOVES occur when the backbones of the strand of DNA are close together ○ MAJOR GROOVES occur when the backbones of the strand of the DNA are far apart, acts as an opening for proteins All grooves must have a 0.1 difference in Angstrom (3.4 & 3.3) to prevent a snap away from the double helix shape 10-11 base pairs per 360 degrees Adenosine Triphosphate (ATP) A nucleotide that consists of three main structures ○ Adenine (nitrogenous base) ○ Ribose (sugar) ○ Chain of three phosphate groups Important source of energy for cellular processes Complicated example of a organic phosphate Contains of an organic molecule called adenosine, attached to a string of three phosphate groups STEM 12-Walpole, General Biology Academics Committee | Page 25 of 29  Biomolecules General Biology 1 | STEM 12-Walpole The outer phosphate may split off as a result of reaction with water (hydrolysis). This turns the ATP into ADP (adenosine diphosphate), which releases energy that can be used by the cell ATP powers cellular processes by transferring a phosphate group to another molecule (phosphorylation) ○ Carried out by special enzymes that couple the release of energy and bring it to cellular activities that require it Guanosine Triphosphate (GTP) Nucleotide that is similar to ATP in structure and cellular function Composed of guanine (instead of adenine in ATP), ribose, and three phosphate groups Can be used to generate ATP molecules or directly power work in the cell Cytidine Triphosphate (CTP) Like ATP and GTP, contains ribose and three phosphate groups, but instead has cytosine as its nitrogenous Similar to ATP, it is a high-energy molecule, but is limited to a smaller range of metabolic reactions Coenzyme in metabolic reactions like the synthesis of glycerophospholipids Substrate in the synthesis of RNA STEM 12-Walpole, General Biology Academics Committee | Page 26 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Thymidine Triphosphate (TTP) AKA deoxythymidine triphosphate (dTTP) ○ However, is the only one of the four nucleoside triphosphates that does not always have the deoxy- prefix Synthesized via the methylation of dUMP via thymidylate synthase Ends of a DNA strand (5’ to 3’) Because DNA is read in a specific direction, each end of a DNA chain is represented by a number, either end is named 3’ (three prime) or 5’ (five prime) These numbers refer to the nth carbon atom in a deoxyribose sugar molecule that a phosphate group binds to Bases in the DNA are read from 5’ to 3’ ○ On the 5’ carbon of its terminal sugar, the 5’ end has a phosphate group ○ On the 3’ carbon of its terminal sugar, the 3’ end has a free hydroxyl group STEM 12-Walpole, General Biology Academics Committee | Page 27 of 29  Biomolecules General Biology 1 | STEM 12-Walpole Antiparallel orientation Describes the opposite orientations of two strands of a DNA double helix (as seen above) ○ The 5’ end of one strand aligns with the 3’ end of the opposite strand and vice versa STEM 12-Walpole, General Biology Academics Committee | Page 28 of 29  Biomolecules General Biology 1 | STEM 12-Walpole BIOETHICS Autonomy Respect to one’s decision However, there are conditions in which autonomy can be overruled: ○ If the person is not in their right state of mind Take note: Presence of a diagnosis for a mental condition does not equate to not having a right state of mind. ○ If the person has undeveloped mental faculties; if the brain is not fully developed yet to make sound decisions In the Philippines, 18 years old is considered the earliest age in which one’s mental faculties can be deemed fully developed. However, this is debatable in court. ○ If the person is not fully informed of the entirety of the case or their condition Beneficence If you can do something to improve the situation, do it. ○ If you do not, you are violating the principle of beneficence. On the other hand, if you are not licensed to do something but you still did it, you can be sued. Remember: Doing the procedure and being sued will NOT violate bioethics *may correct in test questions Non-Maleficence Not intentionally causing harm Doing necessary harm if it means reducing harm ultimately or in the long-run; choose the action that causes the least harm Justice Just and equal opportunities for all Prioritizes those: ○ With the least experience of life ○ With the capacity to promote life (e.g. pregnant women, skilled people, etc.) ○ However, take note that, in most cases, it is a case-to-case basis! Remember: Goal of Bioethics: to save life STEM 12-Walpole, General Biology Academics Committee | Page 29 of 29